Class
AnnotationStoreElementRepresents an annotation of a genomic feature.
Defined in | <seqan/store.h> |
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Signature |
template <typename TPos[, typename TSpec]>
struct AnnotationStoreElement;
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Member Function Overview
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AnnotationStoreElement::AnnotationStoreElement();
Constructor.
Member Typedef Overview
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typedef (...) TAnnotationStoreElement::TId;
Type of annotationId and contigId. -
typedef (...) TAnnotationStoreElement::TPos;
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typedef (...) TAnnotationStoreElement::TValues;
Member Variable Overview
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TPos AnnotationStoreElement::beginPos
Begin position of the annotation in gap space. -
TId AnnotationStoreElement::contigId
Refers to the contig in contigStore that the annotation is part of. -
TPos AnnotationStoreElement::endPos
End position of the annotation in gap space. -
TId AnnotationStoreElement::INVALID_ID
Constant to represent an invalid id. -
TId AnnotationStoreElement::INVALID_POS
Constant to represent an invalid position. -
TId AnnotationStoreElement::lastChildId
The id of the parent annotation. -
TId AnnotationStoreElement::nextSiblingId
The id of the right sibling annotation. -
TId AnnotationStoreElement::parentId
The id of the parent annotation. -
TId AnnotationStoreElement::typeId
Refers to an entry in the annotationTypeStore. -
TValues AnnotationStoreElement::values
StringSet that stores additional values addressed by keyId.
Detailed Description
Value type of the annotationStore stirng. The id of an annotation (aka annotationId) is not stored explicitly as it is implicitly given byt he position in the annotationStore.
Member Functions Detail
AnnotationStoreElement::AnnotationStoreElement();
The default constructor sets all members to INVALID_ID and beginPos and endPos to INVALID_POS.
Data Races
Member Typedef Detail
typedef (...) TAnnotationStoreElement::TId;
TId is the result of Id<AnnotationStoreElement<> >::Type, see Id.
typedef (...) TAnnotationStoreElement::TPos;
typedef (...) TAnnotationStoreElement::TValues;
Member Variables Detail
TPos AnnotationStoreElement::beginPos
If endPos < beginPos then the annotation feature is located on the reverse strand where beginPos and endPos are the corresponding positions on the forward strand.
TId AnnotationStoreElement::contigId
TPos AnnotationStoreElement::endPos
If endPos < beginPos then the annotation feature is located on the reverse strand where beginPos and endPos are the corresponding positions on the forward strand.
TId AnnotationStoreElement::INVALID_ID
TId AnnotationStoreElement::INVALID_POS
TId AnnotationStoreElement::lastChildId
TId AnnotationStoreElement::nextSiblingId
TId AnnotationStoreElement::parentId
TId AnnotationStoreElement::typeId
There are some type ids predefined for commonly used types, e.g. $ANNO_GENE$. See FragmentStore::PredefinedAnnotationTypes.
TValues AnnotationStoreElement::values
The GFF and FTF file formats allow to define user-specific key-value pairs. The set of all keys addressed by keyId are stored in annotationKeyStore.